A cleaner separation-purification process without both conventional molecular distillation and chromatographic separation was developed and used to produce high-purity natural lipophilic phenolic compounds from by-products of vegetable oil refining. The key technology is a novel purification method using a weakly basic resin with acidity between those of impurity component with carboxylic acid group and a desired component with phenolic hydroxyl group as the adsorbent, which enables complete removal of only impurity component from the mixture. By combining the purification method with the separation process previously reported (Hiromori et al., 2015), the total process consisted of three columns packed with different types of ion-exchange resins (strongly acidic resin, strongly basic resin and weakly basic resin). In order to recover vitamin E (tocopherol, tocotrienol), the most prominent natural lipophilic phenolic compounds, a mixture of the by-product, deodorizer distillate from rice bran, and ethanol was supplied to the first and second columns, which were connected in series, and vitamin E selectively adsorbed on the resin. Next, a desorption solution was supplied to the second column connected with third column, and vitamin E (purity >98 wt%) was eluted. The yield of tocopherol was about 100% without thermal decomposition, which was much higher than the yield of about 50% obtained by a conventional method with molecular distillation. The yield of tocotrienol, which has lower thermal stability than tocopherol, was about 71%, whereas that of the conventional method was about 29%. The quantities of raw material and solvent, and the energy consumption to produce 1 kg of high purity vitamin E in this process were drastically reduced compared with the conventional process.